There is a good deal of uncertainty regarding the detailed evolution of the genus Acacia and the different sections of subgenus Phyllodineae in Australia. The earliest fossil record is of pollin from the late Eocene (about 40 million years ago) from south-western Australia⁶⁸. There appears to have been a worldwide expansion of the genus at the beginning of the Miocene (during mid-Tertiary times some 23 million years ago),⁶⁶ and it is during this time that the world wide cooling began, which probably led to drier climates. This would favour the diversification and spread of genera such as Acacia.

Pedley suggests the following scenario.⁶⁵ The plants which gave rise to the acacias originated in the tropical areas of the African-South American part of Gondwana. Subgenera Acacia and Aculeiferum had separated from the proto-Acacia ancestor prior to the separation of Africa and South America (in the Upper Cretaceous period). By the time India began its separation from north-western Australia (in the Cretaceous) these two subgenera were present in India and subgenus Phyllodineae was actively evolving from subgenus Aculeiferum. The evolving Phyllodineae subgenus was possibly dispersing into northern Australia, along with a few early species of subgenus Acacia. These invading acacias would have taken advantage of the drier areas which would have existed between the widespread rainforests.

Carolin⁶⁷, in reviewing the phytogeography of Australian arid plants suggests that arid areas have existed in Australia since the beginning of the Tertiary, even though much of Australia was covered by a type of rainforest vegetation. Further, Truswell and Harris⁶⁶ point out that the deep weathering of some soils which took place in the early Tertiary would have resulted in low nutrient soils and plants adapted to these would develop xeromorphic adaptations, and Truswell^68:554 concludes that sclerophylly probably developed in Australia during the late Eocene, some 40 million years ago. As Australia began its drift into lower latitudes after its separation from Antarctica, the drier areas expanded and spread southwards, enabling the early stock of acacias to diversify and spread into the newly created woodlands and semi-arid and arid regions to the south. The Juliflorae and Plurinerves most likely evolved at this time and are regarded by Pedley to be the most primitive group existing today. From these the other phyllodinous species evolved and spread into the expanding arid regions about the time of the mid-Tertiary. Eventually they occupied most of southern Australia including Tasmania. From these evolved the Pulchellae in south-western Australia, whilst in eastern Australia the Botrycephalae evolved from the ‘racemose’ group of the ‘uninerved’ phyllodinous types. However, uncertainty concerns the Botrycephalae. Some botanists suggest that it is the most recently evolved group, whilst others regard it as a much earlier group from which the ‘uninerved phyllodinous’ species evolved. Either of these evolutionary path can be accommodated within the early Australian Tertiary environment.

Most botanists seem to agree that Acacia has been in Australia for a longer time than the fossil record indicates. Noting that Acacia has a low dispersion ability so that trans-oceanic migration would be difficult, it is argued that the phyllodinous acacias at least, were in Australia as part of the original Gondwanan stock of plants, a view echoed elsewhere⁶⁹.